cgamm: Constrained Generalized Additive Mixed-Effects Model Fitting

In cgam: Constrained Generalized Additive Model

Constrained Generalized Additive Mixed-Effects Model Fitting

Description

This routine is an addition to the main routine cgam in this package. A random-intercept component is included in a cgam model.

Usage

cgamm(formula, nsim = 0, family = gaussian(), cpar = 1.2, data = NULL, weights = NULL,
sc_x = FALSE, sc_y = FALSE, bisect = TRUE, reml = TRUE, nAGQ = 1L)

Arguments

formula	A formula object which gives a symbolic description of the model to be fitted. It has the form "response ~ predictor + (1|id)", where id is the label for a group effect. For now, only gaussian responses are considered and this routine only includes a random-intercept effect. See cgam for more details.
nsim	The number of simulations used to get the cic parameter. The default is nsim = 0.
family	A parameter indicating the error distribution and link function to be used in the model. For now, the options are family = gaussian() and family = binomial().
cpar	A multiplier to estimate the model variance, which is defined as \sigma^2 = SSR / (n - cpar * edf). SSR is the sum of squared residuals for the full model and edf is the effective degrees of freedom. The default is cpar = 1.2. The user-defined value must be between 1 and 2. See Meyer, M. C. and M. Woodroofe (2000) for more details.
data	An optional data frame, list or environment containing the variables in the model. The default is data = NULL.
weights	An optional non-negative vector of "replicate weights" which has the same length as the response vector. If weights are not given, all weights are taken to equal 1. The default is weights = NULL.
sc_x	Logical flag indicating if or not continuous predictors are normalized. The default is sc_x = FALSE.
sc_y	Logical flag indicating if or not the response variable is normalized. The default is sc_y = FALSE.
bisect	If bisect = TRUE, a 95 percent confidence interval will be found for the variance ratio parameter by a bisection method.
reml	If reml = TRUE, restricted maximum likelihood (REML) method will be used to find estimates instead of maximum likelihood estimation (MLE).
nAGQ	Integer scalar - the number of points per axis for evaluating the adaptive Gauss-Hermite approximation to the log-likelihood. Defaults to 1, corresponding to the Laplace approximation. Values greater than 1 produce greater accuracy in the evaluation of the log-likelihood at the expense of speed.

Value

muhat	The fitted fixed-effect term.
ahat	A vector of estimated random-effect terms.
sig2hat	Estimate of the variance (\sigma^2) of between-cluster error terms.
siga2hat	Estimate of the variance (\sigma_a^2) of within-cluster error terms.
thhat	Estimate of the ratio (\theta) of two variances.
pv.siga2	p-value of the test H_0: \sigma_a^2=0
ci.siga2	95 percent confidence interval for the variance of within-cluster error terms.
ci.th	95 percent confidence interval for ratio of two variances.
ci.rho	95 percent confidence interval for intraclass correlation coefficient.
ci.sig2	95 percent confidence interval for the variance of between-cluster error terms.
call	The matched call.

Author(s)

Xiyue Liao

Examples

# Example 1 (family = gaussian).

# simulate a balanced data set with 30 clusters
# each cluster has 30 data points
	n <- 30
	m <- 30

# the standard deviation of between cluster error terms is 1
# the standard deviation of within cluster error terms is 2
	sige <- 1
	siga <- 2

# generate a continuous predictor
	x <- 1:(m*n)
	for(i in 1:m) {
		x[(n*(i-1)+1):(n*i)] <- round(runif(n), 3)
	}
# generate a group factor
	group <- trunc(0:((m*n)-1)/n)+1

# generate the fixed-effect term
	mu <- 10*exp(10*x-5)/(1+exp(10*x-5))

# generate the random-intercept term asscosiated with each group
	avals <- rnorm(m, 0, siga)

# generate the response
	y <- 1:(m*n)
	for(i in 1:m){
		y[group == i] <- mu[group == i] + avals[i] + rnorm(n, 0, sige)
	}

# use REML method to fit the model
	ans <- cgamm(y ~ s.incr(x) + (1|group), reml=TRUE)
	summary(ans)
	anova(ans)

	muhat <- ans$muhat
	plot(x, y, col = group, cex = .6)
	lines(sort(x), mu[order(x)], lwd = 2)
	lines(sort(x), muhat[order(x)], col = 2, lty = 2, lwd = 2)
	legend("topleft", bty = "n", c("true fixed-effect term", "cgamm fit"),
	col = c(1, 2), lty = c(1, 2), lwd = c(2, 2))

# Example 2 (family = binomial).
# simulate a balanced data set with 20 clusters
# each cluster has 20 data points

  n <- 20
  m <- 20#
  N <- n*m

  # siga is the sd for the random intercept
  siga <- 1

# generate a group factor
  group <- trunc(0:((m*n)-1)/n)+1
  group <- factor(group)

# generate the random-intercept term asscosiated with each group
  avals <- rnorm(m,0,siga)

# generate the fixed-effect mean term: mu, systematic term: eta and the response: y
  x <- runif(m*n)
  mu <- 1:(m*n)
  y <- 1:(m*n)

  eta <- 2 * (1 + tanh(7 * (x - .8))) - 2
  eta0 <- eta
  for(i in 1:m){eta[group == i] <- eta[group == i] + avals[i]}
  for(i in 1:m){mu[group == i] <- 1 - 1 / (1 + exp(eta[group == i]))}
  for(i in 1:m){y[group == i] <- rbinom(n, size = 1, prob = mu[group == i])}
  dat <- data.frame(x = x, y = y, group = group)
  ansc <- cgamm(y ~ s.incr.conv(x) + (1|group),
  family = binomial(link = "logit"), reml = FALSE, data = dat)
  summary(ansc)
  anova(ansc)

cgam documentation built on Aug. 10, 2023, 5:11 p.m.